Legacy-contaminated sites act as significant sources of mercury (Hg) to their surrounding surface and underground environments. Intensified extreme precipitation is posing great threats to the environment and human health by changing the fate of pollutants, yet little is known about its effect on the vertical migration and methylation of Hg in contaminated sites. Here, we applied a range of simulated extreme precipitation patterns (frequency and intensity) to column leaching assays with soils collected near a contaminated site. We observed that precipitation with high frequency but low intensity resulted in more vertical migration of Hg through the soil profile than that with low frequency but high intensity. The majority (> 90%) of leached Hg was prone to migrate vertically within the top 10 cm of the soil profile. Furthermore, rainfall stimulated microbial Hg methylation, as demonstrated by enhanced production of methylmercury (MeHg) in both simulated and field-contaminated soils. We identified specific microbial taxa including Geobacteraceae, Desulfuromonadaceae, Syntrophaceae, Oscillospiraceae, and Methanomicrobiaceae as key predictors of MeHg production, which differed from those typically observed in overlying water of croplands. Particularly, the relative abundance of these dominant Hg methylators significantly increased during rainfall-induced leaching compared to that of the control, suggesting the crucial yet previously overlooked impacts of increased precipitation events on the process of microbial Hg methylation in industry-contaminated sites. Given the rising incidences of extreme precipitation events worldwide due to climate change, this study highlights the significance of assessing Hg mobility and microbial transformation in legacy contaminated sites.